We have been developing an electron diffractive imaging method by using “low-voltage” electron beam to analyze the atomic structures of light-element materials. Light elements, which are considered to be the key materials in the fields of sustainable energy and environmental engineering, are cumbersome materials for conventional electron microscopy because they are damaged easily by “high-voltage” electron beam irradiation. The electron diffractive imaging method, which reconstructs the structures of specimens from electron diffraction pattern via iterative phase retrieval, can obtain high-resolution images avoiding lens aberrations and also obtain phase images. By using a prototype microscope, characteristic features (outer and inner diameters, number of walls) of multiwall carbon nanotube were reconstructed from a diffraction pattern recorded at 20 kV. To solve difficulties that arose in the prototype, we developed an electron diffraction microscope based on a conventional scanning electron microscope. Using this microscope, atomic arrangement of a single wall carbon nanotube (SWCNT) was reconstructed from a 30-kV diffraction pattern. Before the iterative phase retrieval, image processing to reduce noises in the diffraction pattern was executed. In the reconstructed SWCNT image, intensity difference between single isolated atoms and two overlapped atoms could be divided.